R: User-Defined Link Communities

newLinkCommsAt {linkcomm} | R Documentation

## User-Defined Link Communities

### Description

This function allows the user to extract link communities by cutting the dendrogram at a specified height.

### Usage

    newLinkCommsAt(x, cutat = 0.5)

### Arguments

`x` | An object of class `linkcomm`.
`cutat` | A numerical value indicating the height at which to cut the dendrogram. Defaults to 0.5.

### Details

Users may wish to explore the communities formed by cutting the dendrogram higher or lower than the maximum partition density height. After cutting at a new height, the `pdmax` value in the resulting object will be set to the `cutat` value used by the user, only to distinguish the new object from the one generated by the link communities algorithm (the global partition density maximum does not change).

### Value

An object of class `linkcomm`, which is a list containing the following components:

`numbers` | An integer vector with the number of edges, nodes, and communities.
`hclust` | An object of class `hclust`, which contains information about the hierarchical clustering of links.
`pdmax` | A numerical value indicating the height of the dendrogram at which the partition density is maximised.
`pdens` | A numerical matrix with 2 columns; the first is the heights at which clusters appear and the second is the partition density.
`nodeclusters` | A data frame consisting of 2 columns; the first contains node names, and the second contains single community IDs for each node. All communities and their nodes are represented, but not necessarily all nodes.
`clusters` | A list of integer vectors containing the link IDs that belong to each community. Community IDs are the numerical position of the communities in the list.
`edges` | A data frame with 3 columns; the first two contain nodes that interact with each other, and the third is an integer vector of community IDs indicating community membership for each link.
`numclusters` | A named integer vector. Names are node names and integer values are the number of communities to which each node belongs.
`clustsizes` | A named integer vector. Names are community IDs and integer values indicate the number of nodes that belong in each community.
`igraph` | An object of class `igraph`. The network is represented here as an `igraph` object.
`edgelist` | A character matrix with 2 columns containing the nodes that interact with each other.
`directed` | Logical indicating whether the network is directed.
`bipartite` | Logical indicating whether the network is bipartite.

### Note

After cutting at a new height, the `pdmax` value in the resulting object will be set to the `cutat` value used by the user, only to distinguish the new object from the one generated by the link communities algorithm (the global partition density maximum does not change).

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

### See Also

`getLinkCommunities`

### Examples

    ## Generate graph and extract link communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)

    ## User defined communities.
    lc2 <- newLinkCommsAt(lc, cutat = 0.8)

[Package linkcomm version 1.0-14 Index]